The effects of converting native forests to livestock systems on soil C, N and P contents across various climatic zones are not well understood for the tropical region. The goal of this study was to test how soil C, N and P dynamics are affected by the land-use change from natural forests to livestock production systems (extensive pasture and intensive silvopastoral systems) across a rainfall gradient of 1611–711 mm per year in the Mexican tropics. A total of 15 soil-based biogeochemical metrics were measured in samples collected during the dry and rainy seasons in livestock systems and mature forests for land-use and intersite comparisons of the nutrient status. Our results show that land-use change from natural forests to livestock production systems had a negative effect on soil C, N and P contents. In general, soil basal respiration and C-acquiring enzyme activities increased under livestock production systems. Additionally, reduction in mean annual rainfall affected moisture-sensitive biogeochemical processes affecting the C, N and P dynamics. Our findings imply that land-use changes alter soil C, N and P dynamics and contents, with potential negative consequences for the sustainability of livestock production systems in the tropical regions of Mexico investigated.